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annotate snpSift_rmInfo.xml @ 4:b04635ebfab0 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 9d2052269bfbca81a5f9cd10c3153e611358a329
author iuc
date Tue, 24 Oct 2017 07:28:17 -0400
parents 20c7d583fec1
children 09d6806c609e
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20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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1 <tool id="snpSift_rmInfo" name="SnpSift rmInfo" version="@WRAPPER_VERSION@.0">
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2 <description>remove INFO field annotations</description>
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3 <macros>
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4 <import>snpSift_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="stdio" />
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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8 <expand macro="version_command" />
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9 <command><![CDATA[
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10 SnpSift -Xmx2G rmInfo
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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11 '$input'
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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12 #echo ' '.join($info_fields.split(','))
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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13 > '$output'
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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14 ]]></command>
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15 <inputs>
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16 <param name="input" type="data" format="vcf" label="Variant input file in VCF format"/>
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17 <param name="info_fields" type="text" value="" label="Info fields to remove, e.g. EFF">
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18 <help>Separate multiple INFO fields with a comma, e.g.: EFF,DP</help>
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19 <validator type="empty_field" />
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20 </param>
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21 </inputs>
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22 <outputs>
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23 <data name="output" format="vcf" />
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24 </outputs>
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25 <tests>
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26 <test>
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27 <param name="input" ftype="vcf" value="test_rmInfo.vcf"/>
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28 <param name="info_fields" value="EFF"/>
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29 <output name="output">
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30 <assert_contents>
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31 <has_text text="DP=29" />
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32 <not_has_text text="EFF=EXON" />
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33 </assert_contents>
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34 </output>
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35 </test>
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36 </tests>
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37 <help><![CDATA[
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38 This command removes INFO fields from a VCF file (i.e. removes annotations)
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39
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40 Removing INFO fields is usually done because you want to re-annotate the VCF file, thus removing old INFO fields in order to add new ones later.
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41
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42 SnpEff & SnpSift only add annotations and do not change current ones. So, in order to re-annotate a file, you should first remove the old annotations and then re-annotate.
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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43 The reason for this behavior is simply because replacing annotation values is considered a bad practice. Imagine that you have a VCF entry in your re-annotated file having the value "AA=1": How do you know if this is from the old annotations or from the new ones? This confusion often leads to problems in downstream steps of your pipelines, so it's better to avoid the problem by first removing all the previous annotations and then adding the new ones.
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45 @EXTERNAL_DOCUMENTATION@
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46 - http://snpeff.sourceforge.net/SnpSift.html#rmInfo
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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47 ]]></help>
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48 <expand macro="citations" />
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49 </tool>